基于FPGA的分子动力学模拟交互控制系统

摘要/Abstract

摘要： 在分子动力学模拟系统中，实现分子间短程力的计算需要频繁地传输与大量的粒子数据访问。为了减轻CPU的计算负载，可以使用FPGA加速计算。但是，在基于FPGA的分子动力学模拟系统中，短程力计算模块面临巨大的数据传输压力以及访存冲突问题。针对这些问题，基于FPGA上有限的硬件资源，提出一种交互控制系统。该系统由取数控制模块与粒子数据解析模块组成。整个系统通过合理的数据编排以及2个模块的协同工作，实现粒子数据从片上存储到短程力计算模块的快速可靠的传输。通过硬件仿真和板级实验验证了该系统在处理粒子数据过程中的有效性和可靠性。

关键词: 分子动力学, 短程力, 交互控制系统, 现场可编程门阵列, 并行计算

Abstract: In molecular dynamics simulation systems, the computation of range-limited forces between molecules requires frequent transfers and large amounts of particle data access. To reduce the computational load on the CPU, FPGAs can be used to accelerate the computation. However, in the FPGA-based molecular dynamics simulation system, the range-limited force calculation module faces huge data transfer pressure and access conflict problems. To address these problems, an interactive control system is designed based on the limited hardware resources on FPGAs. The system consists of a fetch control module and a particle data parsing module. The whole system achieves fast and reliable transmission of particle data from on-chip storage to the range-limited force calculation module through reasonable data arrangement and cooperative work of the two modules. The effectiveness and reliability of the system in processing particle data are further verified by hardware simulation and board-level experiments.

Key words: molecular dynamics, range-limited force, interactive control system, Field Programmable Gate Array （ FPGA）, parallel computing

王鑫, 吴俊辉, . 基于FPGA的分子动力学模拟交互控制系统[J]. 计算机与现代化, 2022, 0(09): 25-31.

WANG Xin, WU Jun-hui, . FPGA-based Interactive Control System for Molecular Dynamics Simulation[J]. Computer and Modernization, 2022, 0(09): 25-31.

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